Starting phenix.real_space_refine (version: dev) on Wed Feb 22 01:51:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rib_4887/02_2023/6rib_4887_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rib_4887/02_2023/6rib_4887.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rib_4887/02_2023/6rib_4887.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rib_4887/02_2023/6rib_4887.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rib_4887/02_2023/6rib_4887_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rib_4887/02_2023/6rib_4887_neut.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A ASP 24": "OD1" <-> "OD2" Residue "A ARG 26": "NH1" <-> "NH2" Residue "A ARG 32": "NH1" <-> "NH2" Residue "A ARG 38": "NH1" <-> "NH2" Residue "A GLU 44": "OE1" <-> "OE2" Residue "A GLU 46": "OE1" <-> "OE2" Residue "A ARG 54": "NH1" <-> "NH2" Residue "A ARG 59": "NH1" <-> "NH2" Residue "A ARG 63": "NH1" <-> "NH2" Residue "A ARG 87": "NH1" <-> "NH2" Residue "B ASP 24": "OD1" <-> "OD2" Residue "B ARG 26": "NH1" <-> "NH2" Residue "B ARG 32": "NH1" <-> "NH2" Residue "B ARG 38": "NH1" <-> "NH2" Residue "B GLU 44": "OE1" <-> "OE2" Residue "B GLU 46": "OE1" <-> "OE2" Residue "B ARG 54": "NH1" <-> "NH2" Residue "B ARG 59": "NH1" <-> "NH2" Residue "B ARG 63": "NH1" <-> "NH2" Residue "B ARG 87": "NH1" <-> "NH2" Residue "C ASP 24": "OD1" <-> "OD2" Residue "C ARG 26": "NH1" <-> "NH2" Residue "C ARG 32": "NH1" <-> "NH2" Residue "C ARG 38": "NH1" <-> "NH2" Residue "C GLU 44": "OE1" <-> "OE2" Residue "C GLU 46": "OE1" <-> "OE2" Residue "C ARG 54": "NH1" <-> "NH2" Residue "C ARG 59": "NH1" <-> "NH2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "C ARG 87": "NH1" <-> "NH2" Residue "D ASP 24": "OD1" <-> "OD2" Residue "D ARG 26": "NH1" <-> "NH2" Residue "D ARG 32": "NH1" <-> "NH2" Residue "D ARG 38": "NH1" <-> "NH2" Residue "D GLU 44": "OE1" <-> "OE2" Residue "D GLU 46": "OE1" <-> "OE2" Residue "D ARG 54": "NH1" <-> "NH2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D ARG 63": "NH1" <-> "NH2" Residue "D ARG 87": "NH1" <-> "NH2" Residue "E ASP 24": "OD1" <-> "OD2" Residue "E ARG 26": "NH1" <-> "NH2" Residue "E ARG 32": "NH1" <-> "NH2" Residue "E ARG 38": "NH1" <-> "NH2" Residue "E GLU 44": "OE1" <-> "OE2" Residue "E GLU 46": "OE1" <-> "OE2" Residue "E ARG 54": "NH1" <-> "NH2" Residue "E ARG 59": "NH1" <-> "NH2" Residue "E ARG 63": "NH1" <-> "NH2" Residue "E ARG 87": "NH1" <-> "NH2" Residue "F ASP 24": "OD1" <-> "OD2" Residue "F ARG 26": "NH1" <-> "NH2" Residue "F ARG 32": "NH1" <-> "NH2" Residue "F ARG 38": "NH1" <-> "NH2" Residue "F GLU 44": "OE1" <-> "OE2" Residue "F GLU 46": "OE1" <-> "OE2" Residue "F ARG 54": "NH1" <-> "NH2" Residue "F ARG 59": "NH1" <-> "NH2" Residue "F ARG 63": "NH1" <-> "NH2" Residue "F ARG 87": "NH1" <-> "NH2" Residue "G ASP 24": "OD1" <-> "OD2" Residue "G ARG 26": "NH1" <-> "NH2" Residue "G ARG 32": "NH1" <-> "NH2" Residue "G ARG 38": "NH1" <-> "NH2" Residue "G GLU 44": "OE1" <-> "OE2" Residue "G GLU 46": "OE1" <-> "OE2" Residue "G ARG 54": "NH1" <-> "NH2" Residue "G ARG 59": "NH1" <-> "NH2" Residue "G ARG 63": "NH1" <-> "NH2" Residue "G ARG 87": "NH1" <-> "NH2" Residue "H ASP 24": "OD1" <-> "OD2" Residue "H ARG 26": "NH1" <-> "NH2" Residue "H ARG 32": "NH1" <-> "NH2" Residue "H ARG 38": "NH1" <-> "NH2" Residue "H GLU 44": "OE1" <-> "OE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H ARG 54": "NH1" <-> "NH2" Residue "H ARG 59": "NH1" <-> "NH2" Residue "H ARG 63": "NH1" <-> "NH2" Residue "H ARG 87": "NH1" <-> "NH2" Residue "I ASP 24": "OD1" <-> "OD2" Residue "I ARG 26": "NH1" <-> "NH2" Residue "I ARG 32": "NH1" <-> "NH2" Residue "I ARG 38": "NH1" <-> "NH2" Residue "I GLU 44": "OE1" <-> "OE2" Residue "I GLU 46": "OE1" <-> "OE2" Residue "I ARG 54": "NH1" <-> "NH2" Residue "I ARG 59": "NH1" <-> "NH2" Residue "I ARG 63": "NH1" <-> "NH2" Residue "I ARG 87": "NH1" <-> "NH2" Residue "J ASP 24": "OD1" <-> "OD2" Residue "J ARG 26": "NH1" <-> "NH2" Residue "J ARG 32": "NH1" <-> "NH2" Residue "J ARG 38": "NH1" <-> "NH2" Residue "J GLU 44": "OE1" <-> "OE2" Residue "J GLU 46": "OE1" <-> "OE2" Residue "J ARG 54": "NH1" <-> "NH2" Residue "J ARG 59": "NH1" <-> "NH2" Residue "J ARG 63": "NH1" <-> "NH2" Residue "J ARG 87": "NH1" <-> "NH2" Residue "K ASP 24": "OD1" <-> "OD2" Residue "K ARG 26": "NH1" <-> "NH2" Residue "K ARG 32": "NH1" <-> "NH2" Residue "K ARG 38": "NH1" <-> "NH2" Residue "K GLU 44": "OE1" <-> "OE2" Residue "K GLU 46": "OE1" <-> "OE2" Residue "K ARG 54": "NH1" <-> "NH2" Residue "K ARG 59": "NH1" <-> "NH2" Residue "K ARG 63": "NH1" <-> "NH2" Residue "K ARG 87": "NH1" <-> "NH2" Residue "L ASP 24": "OD1" <-> "OD2" Residue "L ARG 26": "NH1" <-> "NH2" Residue "L ARG 32": "NH1" <-> "NH2" Residue "L ARG 38": "NH1" <-> "NH2" Residue "L GLU 44": "OE1" <-> "OE2" Residue "L GLU 46": "OE1" <-> "OE2" Residue "L ARG 54": "NH1" <-> "NH2" Residue "L ARG 59": "NH1" <-> "NH2" Residue "L ARG 63": "NH1" <-> "NH2" Residue "L ARG 87": "NH1" <-> "NH2" Residue "M ASP 24": "OD1" <-> "OD2" Residue "M ARG 26": "NH1" <-> "NH2" Residue "M ARG 32": "NH1" <-> "NH2" Residue "M ARG 38": "NH1" <-> "NH2" Residue "M GLU 44": "OE1" <-> "OE2" Residue "M GLU 46": "OE1" <-> "OE2" Residue "M ARG 54": "NH1" <-> "NH2" Residue "M ARG 59": "NH1" <-> "NH2" Residue "M ARG 63": "NH1" <-> "NH2" Residue "M ARG 87": "NH1" <-> "NH2" Residue "N ASP 24": "OD1" <-> "OD2" Residue "N ARG 26": "NH1" <-> "NH2" Residue "N ARG 32": "NH1" <-> "NH2" Residue "N ARG 38": "NH1" <-> "NH2" Residue "N GLU 44": "OE1" <-> "OE2" Residue "N GLU 46": "OE1" <-> "OE2" Residue "N ARG 54": "NH1" <-> "NH2" Residue "N ARG 59": "NH1" <-> "NH2" Residue "N ARG 63": "NH1" <-> "NH2" Residue "N ARG 87": "NH1" <-> "NH2" Residue "O ASP 24": "OD1" <-> "OD2" Residue "O ARG 26": "NH1" <-> "NH2" Residue "O ARG 32": "NH1" <-> "NH2" Residue "O ARG 38": "NH1" <-> "NH2" Residue "O GLU 44": "OE1" <-> "OE2" Residue "O GLU 46": "OE1" <-> "OE2" Residue "O ARG 54": "NH1" <-> "NH2" Residue "O ARG 59": "NH1" <-> "NH2" Residue "O ARG 63": "NH1" <-> "NH2" Residue "O ARG 87": "NH1" <-> "NH2" Residue "P ASP 24": "OD1" <-> "OD2" Residue "P ARG 26": "NH1" <-> "NH2" Residue "P ARG 32": "NH1" <-> "NH2" Residue "P ARG 38": "NH1" <-> "NH2" Residue "P GLU 44": "OE1" <-> "OE2" Residue "P GLU 46": "OE1" <-> "OE2" Residue "P ARG 54": "NH1" <-> "NH2" Residue "P ARG 59": "NH1" <-> "NH2" Residue "P ARG 63": "NH1" <-> "NH2" Residue "P ARG 87": "NH1" <-> "NH2" Residue "Q ASP 24": "OD1" <-> "OD2" Residue "Q ARG 26": "NH1" <-> "NH2" Residue "Q ARG 32": "NH1" <-> "NH2" Residue "Q ARG 38": "NH1" <-> "NH2" Residue "Q GLU 44": "OE1" <-> "OE2" Residue "Q GLU 46": "OE1" <-> "OE2" Residue "Q ARG 54": "NH1" <-> "NH2" Residue "Q ARG 59": "NH1" <-> "NH2" Residue "Q ARG 63": "NH1" <-> "NH2" Residue "Q ARG 87": "NH1" <-> "NH2" Residue "R ASP 24": "OD1" <-> "OD2" Residue "R ARG 26": "NH1" <-> "NH2" Residue "R ARG 32": "NH1" <-> "NH2" Residue "R ARG 38": "NH1" <-> "NH2" Residue "R GLU 44": "OE1" <-> "OE2" Residue "R GLU 46": "OE1" <-> "OE2" Residue "R ARG 54": "NH1" <-> "NH2" Residue "R ARG 59": "NH1" <-> "NH2" Residue "R ARG 63": "NH1" <-> "NH2" Residue "R ARG 87": "NH1" <-> "NH2" Residue "S ASP 24": "OD1" <-> "OD2" Residue "S ARG 26": "NH1" <-> "NH2" Residue "S ARG 32": "NH1" <-> "NH2" Residue "S ARG 38": "NH1" <-> "NH2" Residue "S GLU 44": "OE1" <-> "OE2" Residue "S GLU 46": "OE1" <-> "OE2" Residue "S ARG 54": "NH1" <-> "NH2" Residue "S ARG 59": "NH1" <-> "NH2" Residue "S ARG 63": "NH1" <-> "NH2" Residue "S ARG 87": "NH1" <-> "NH2" Residue "T ASP 24": "OD1" <-> "OD2" Residue "T ARG 26": "NH1" <-> "NH2" Residue "T ARG 32": "NH1" <-> "NH2" Residue "T ARG 38": "NH1" <-> "NH2" Residue "T GLU 44": "OE1" <-> "OE2" Residue "T GLU 46": "OE1" <-> "OE2" Residue "T ARG 54": "NH1" <-> "NH2" Residue "T ARG 59": "NH1" <-> "NH2" Residue "T ARG 63": "NH1" <-> "NH2" Residue "T ARG 87": "NH1" <-> "NH2" Residue "U ASP 24": "OD1" <-> "OD2" Residue "U ARG 26": "NH1" <-> "NH2" Residue "U ARG 32": "NH1" <-> "NH2" Residue "U ARG 38": "NH1" <-> "NH2" Residue "U GLU 44": "OE1" <-> "OE2" Residue "U GLU 46": "OE1" <-> "OE2" Residue "U ARG 54": "NH1" <-> "NH2" Residue "U ARG 59": "NH1" <-> "NH2" Residue "U ARG 63": "NH1" <-> "NH2" Residue "U ARG 87": "NH1" <-> "NH2" Residue "V ASP 24": "OD1" <-> "OD2" Residue "V ARG 26": "NH1" <-> "NH2" Residue "V ARG 32": "NH1" <-> "NH2" Residue "V ARG 38": "NH1" <-> "NH2" Residue "V GLU 44": "OE1" <-> "OE2" Residue "V GLU 46": "OE1" <-> "OE2" Residue "V ARG 54": "NH1" <-> "NH2" Residue "V ARG 59": "NH1" <-> "NH2" Residue "V ARG 63": "NH1" <-> "NH2" Residue "V ARG 87": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 16368 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 744 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 2, 'TRANS': 98} Chain: "B" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 744 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 2, 'TRANS': 98} Chain: "C" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 744 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 2, 'TRANS': 98} Chain: "D" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 744 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 2, 'TRANS': 98} Chain: "E" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 744 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 2, 'TRANS': 98} Chain: "F" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 744 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 2, 'TRANS': 98} Chain: "G" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 744 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 2, 'TRANS': 98} Chain: "H" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 744 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 2, 'TRANS': 98} Chain: "I" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 744 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 2, 'TRANS': 98} Chain: "J" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 744 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 2, 'TRANS': 98} Chain: "K" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 744 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 2, 'TRANS': 98} Chain: "L" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 744 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 2, 'TRANS': 98} Chain: "M" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 744 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 2, 'TRANS': 98} Chain: "N" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 744 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 2, 'TRANS': 98} Chain: "O" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 744 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 2, 'TRANS': 98} Chain: "P" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 744 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 2, 'TRANS': 98} Chain: "Q" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 744 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 2, 'TRANS': 98} Chain: "R" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 744 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 2, 'TRANS': 98} Chain: "S" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 744 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 2, 'TRANS': 98} Chain: "T" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 744 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 2, 'TRANS': 98} Chain: "U" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 744 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 2, 'TRANS': 98} Chain: "V" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 744 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 2, 'TRANS': 98} Time building chain proxies: 9.03, per 1000 atoms: 0.55 Number of scatterers: 16368 At special positions: 0 Unit cell: (49.22, 78.11, 337.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 22 16.00 O 3212 8.00 N 2926 7.00 C 10208 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.36 Conformation dependent library (CDL) restraints added in 2.5 seconds 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3828 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 88 sheets defined 0.0% alpha, 23.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing sheet with id= A, first strand: chain 'A' and resid 20 through 22 removed outlier: 6.854A pdb=" N LEU A 36 " --> pdb=" O VAL A 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 26 through 28 removed outlier: 6.280A pdb=" N LEU A 42 " --> pdb=" O ALA A 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 31 through 33 removed outlier: 6.076A pdb=" N SER A 64 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL A 49 " --> pdb=" O SER A 64 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU A 66 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LYS A 79 " --> pdb=" O VAL A 65 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE A 67 " --> pdb=" O LYS A 79 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL A 81 " --> pdb=" O ILE A 67 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA A 96 " --> pdb=" O VAL A 80 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 54 through 56 removed outlier: 7.486A pdb=" N GLU A 70 " --> pdb=" O VAL A 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 20 through 22 removed outlier: 6.855A pdb=" N LEU B 36 " --> pdb=" O VAL B 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 26 through 28 removed outlier: 6.280A pdb=" N LEU B 42 " --> pdb=" O ALA B 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 31 through 33 removed outlier: 6.076A pdb=" N SER B 64 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N VAL B 49 " --> pdb=" O SER B 64 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU B 66 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LYS B 79 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ILE B 67 " --> pdb=" O LYS B 79 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL B 81 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA B 96 " --> pdb=" O VAL B 80 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 54 through 56 removed outlier: 7.484A pdb=" N GLU B 70 " --> pdb=" O VAL B 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'C' and resid 20 through 22 removed outlier: 6.854A pdb=" N LEU C 36 " --> pdb=" O VAL C 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'C' and resid 26 through 28 removed outlier: 6.280A pdb=" N LEU C 42 " --> pdb=" O ALA C 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'C' and resid 31 through 33 removed outlier: 6.076A pdb=" N SER C 64 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL C 49 " --> pdb=" O SER C 64 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU C 66 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LYS C 79 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE C 67 " --> pdb=" O LYS C 79 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL C 81 " --> pdb=" O ILE C 67 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA C 96 " --> pdb=" O VAL C 80 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 54 through 56 removed outlier: 7.485A pdb=" N GLU C 70 " --> pdb=" O VAL C 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'D' and resid 20 through 22 removed outlier: 6.853A pdb=" N LEU D 36 " --> pdb=" O VAL D 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'D' and resid 26 through 28 removed outlier: 6.280A pdb=" N LEU D 42 " --> pdb=" O ALA D 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'D' and resid 31 through 33 removed outlier: 6.077A pdb=" N SER D 64 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N VAL D 49 " --> pdb=" O SER D 64 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU D 66 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LYS D 79 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE D 67 " --> pdb=" O LYS D 79 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL D 81 " --> pdb=" O ILE D 67 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA D 96 " --> pdb=" O VAL D 80 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 54 through 56 removed outlier: 7.485A pdb=" N GLU D 70 " --> pdb=" O VAL D 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'E' and resid 20 through 22 removed outlier: 6.854A pdb=" N LEU E 36 " --> pdb=" O VAL E 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'E' and resid 26 through 28 removed outlier: 6.280A pdb=" N LEU E 42 " --> pdb=" O ALA E 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'E' and resid 31 through 33 removed outlier: 6.076A pdb=" N SER E 64 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL E 49 " --> pdb=" O SER E 64 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU E 66 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LYS E 79 " --> pdb=" O VAL E 65 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE E 67 " --> pdb=" O LYS E 79 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL E 81 " --> pdb=" O ILE E 67 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA E 96 " --> pdb=" O VAL E 80 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 54 through 56 removed outlier: 7.486A pdb=" N GLU E 70 " --> pdb=" O VAL E 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'F' and resid 20 through 22 removed outlier: 6.855A pdb=" N LEU F 36 " --> pdb=" O VAL F 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'F' and resid 26 through 28 removed outlier: 6.280A pdb=" N LEU F 42 " --> pdb=" O ALA F 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'F' and resid 31 through 33 removed outlier: 6.077A pdb=" N SER F 64 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N VAL F 49 " --> pdb=" O SER F 64 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU F 66 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LYS F 79 " --> pdb=" O VAL F 65 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ILE F 67 " --> pdb=" O LYS F 79 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL F 81 " --> pdb=" O ILE F 67 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA F 96 " --> pdb=" O VAL F 80 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 54 through 56 removed outlier: 7.485A pdb=" N GLU F 70 " --> pdb=" O VAL F 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'G' and resid 20 through 22 removed outlier: 6.854A pdb=" N LEU G 36 " --> pdb=" O VAL G 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'G' and resid 26 through 28 removed outlier: 6.280A pdb=" N LEU G 42 " --> pdb=" O ALA G 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'G' and resid 31 through 33 removed outlier: 6.075A pdb=" N SER G 64 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N VAL G 49 " --> pdb=" O SER G 64 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU G 66 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LYS G 79 " --> pdb=" O VAL G 65 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE G 67 " --> pdb=" O LYS G 79 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL G 81 " --> pdb=" O ILE G 67 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA G 96 " --> pdb=" O VAL G 80 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'G' and resid 54 through 56 removed outlier: 7.486A pdb=" N GLU G 70 " --> pdb=" O VAL G 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'H' and resid 20 through 22 removed outlier: 6.853A pdb=" N LEU H 36 " --> pdb=" O VAL H 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'H' and resid 26 through 28 removed outlier: 6.280A pdb=" N LEU H 42 " --> pdb=" O ALA H 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain 'H' and resid 31 through 33 removed outlier: 6.078A pdb=" N SER H 64 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N VAL H 49 " --> pdb=" O SER H 64 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU H 66 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LYS H 79 " --> pdb=" O VAL H 65 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ILE H 67 " --> pdb=" O LYS H 79 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL H 81 " --> pdb=" O ILE H 67 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA H 96 " --> pdb=" O VAL H 80 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'H' and resid 54 through 56 removed outlier: 7.485A pdb=" N GLU H 70 " --> pdb=" O VAL H 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain 'I' and resid 20 through 22 removed outlier: 6.854A pdb=" N LEU I 36 " --> pdb=" O VAL I 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= AG Processing sheet with id= AH, first strand: chain 'I' and resid 26 through 28 removed outlier: 6.280A pdb=" N LEU I 42 " --> pdb=" O ALA I 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= AH Processing sheet with id= AI, first strand: chain 'I' and resid 31 through 33 removed outlier: 6.076A pdb=" N SER I 64 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N VAL I 49 " --> pdb=" O SER I 64 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU I 66 " --> pdb=" O VAL I 49 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LYS I 79 " --> pdb=" O VAL I 65 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE I 67 " --> pdb=" O LYS I 79 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL I 81 " --> pdb=" O ILE I 67 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA I 96 " --> pdb=" O VAL I 80 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'I' and resid 54 through 56 removed outlier: 7.485A pdb=" N GLU I 70 " --> pdb=" O VAL I 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= AJ Processing sheet with id= AK, first strand: chain 'J' and resid 20 through 22 removed outlier: 6.855A pdb=" N LEU J 36 " --> pdb=" O VAL J 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= AK Processing sheet with id= AL, first strand: chain 'J' and resid 26 through 28 removed outlier: 6.279A pdb=" N LEU J 42 " --> pdb=" O ALA J 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= AL Processing sheet with id= AM, first strand: chain 'J' and resid 31 through 33 removed outlier: 6.076A pdb=" N SER J 64 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N VAL J 49 " --> pdb=" O SER J 64 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU J 66 " --> pdb=" O VAL J 49 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LYS J 79 " --> pdb=" O VAL J 65 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE J 67 " --> pdb=" O LYS J 79 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL J 81 " --> pdb=" O ILE J 67 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA J 96 " --> pdb=" O VAL J 80 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'J' and resid 54 through 56 removed outlier: 7.484A pdb=" N GLU J 70 " --> pdb=" O VAL J 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= AN Processing sheet with id= AO, first strand: chain 'K' and resid 20 through 22 removed outlier: 6.854A pdb=" N LEU K 36 " --> pdb=" O VAL K 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= AO Processing sheet with id= AP, first strand: chain 'K' and resid 26 through 28 removed outlier: 6.280A pdb=" N LEU K 42 " --> pdb=" O ALA K 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= AP Processing sheet with id= AQ, first strand: chain 'K' and resid 31 through 33 removed outlier: 6.075A pdb=" N SER K 64 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL K 49 " --> pdb=" O SER K 64 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU K 66 " --> pdb=" O VAL K 49 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LYS K 79 " --> pdb=" O VAL K 65 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ILE K 67 " --> pdb=" O LYS K 79 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL K 81 " --> pdb=" O ILE K 67 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA K 96 " --> pdb=" O VAL K 80 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'K' and resid 54 through 56 removed outlier: 7.485A pdb=" N GLU K 70 " --> pdb=" O VAL K 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= AR Processing sheet with id= AS, first strand: chain 'L' and resid 20 through 22 removed outlier: 6.853A pdb=" N LEU L 36 " --> pdb=" O VAL L 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= AS Processing sheet with id= AT, first strand: chain 'L' and resid 26 through 28 removed outlier: 6.280A pdb=" N LEU L 42 " --> pdb=" O ALA L 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= AT Processing sheet with id= AU, first strand: chain 'L' and resid 31 through 33 removed outlier: 6.077A pdb=" N SER L 64 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N VAL L 49 " --> pdb=" O SER L 64 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU L 66 " --> pdb=" O VAL L 49 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LYS L 79 " --> pdb=" O VAL L 65 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE L 67 " --> pdb=" O LYS L 79 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL L 81 " --> pdb=" O ILE L 67 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA L 96 " --> pdb=" O VAL L 80 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'L' and resid 54 through 56 removed outlier: 7.485A pdb=" N GLU L 70 " --> pdb=" O VAL L 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= AV Processing sheet with id= AW, first strand: chain 'M' and resid 20 through 22 removed outlier: 6.853A pdb=" N LEU M 36 " --> pdb=" O VAL M 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= AW Processing sheet with id= AX, first strand: chain 'M' and resid 26 through 28 removed outlier: 6.281A pdb=" N LEU M 42 " --> pdb=" O ALA M 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= AX Processing sheet with id= AY, first strand: chain 'M' and resid 31 through 33 removed outlier: 6.076A pdb=" N SER M 64 " --> pdb=" O LEU M 47 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL M 49 " --> pdb=" O SER M 64 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU M 66 " --> pdb=" O VAL M 49 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LYS M 79 " --> pdb=" O VAL M 65 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE M 67 " --> pdb=" O LYS M 79 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL M 81 " --> pdb=" O ILE M 67 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA M 96 " --> pdb=" O VAL M 80 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'M' and resid 54 through 56 removed outlier: 7.485A pdb=" N GLU M 70 " --> pdb=" O VAL M 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= AZ Processing sheet with id= BA, first strand: chain 'N' and resid 20 through 22 removed outlier: 6.855A pdb=" N LEU N 36 " --> pdb=" O VAL N 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= BA Processing sheet with id= BB, first strand: chain 'N' and resid 26 through 28 removed outlier: 6.279A pdb=" N LEU N 42 " --> pdb=" O ALA N 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= BB Processing sheet with id= BC, first strand: chain 'N' and resid 31 through 33 removed outlier: 6.076A pdb=" N SER N 64 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL N 49 " --> pdb=" O SER N 64 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU N 66 " --> pdb=" O VAL N 49 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LYS N 79 " --> pdb=" O VAL N 65 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE N 67 " --> pdb=" O LYS N 79 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL N 81 " --> pdb=" O ILE N 67 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA N 96 " --> pdb=" O VAL N 80 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'N' and resid 54 through 56 removed outlier: 7.485A pdb=" N GLU N 70 " --> pdb=" O VAL N 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= BD Processing sheet with id= BE, first strand: chain 'O' and resid 20 through 22 removed outlier: 6.854A pdb=" N LEU O 36 " --> pdb=" O VAL O 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= BE Processing sheet with id= BF, first strand: chain 'O' and resid 26 through 28 removed outlier: 6.280A pdb=" N LEU O 42 " --> pdb=" O ALA O 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= BF Processing sheet with id= BG, first strand: chain 'O' and resid 31 through 33 removed outlier: 6.076A pdb=" N SER O 64 " --> pdb=" O LEU O 47 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL O 49 " --> pdb=" O SER O 64 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU O 66 " --> pdb=" O VAL O 49 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LYS O 79 " --> pdb=" O VAL O 65 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE O 67 " --> pdb=" O LYS O 79 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL O 81 " --> pdb=" O ILE O 67 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA O 96 " --> pdb=" O VAL O 80 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'O' and resid 54 through 56 removed outlier: 7.486A pdb=" N GLU O 70 " --> pdb=" O VAL O 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= BH Processing sheet with id= BI, first strand: chain 'P' and resid 20 through 22 removed outlier: 6.853A pdb=" N LEU P 36 " --> pdb=" O VAL P 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= BI Processing sheet with id= BJ, first strand: chain 'P' and resid 26 through 28 removed outlier: 6.279A pdb=" N LEU P 42 " --> pdb=" O ALA P 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= BJ Processing sheet with id= BK, first strand: chain 'P' and resid 31 through 33 removed outlier: 6.077A pdb=" N SER P 64 " --> pdb=" O LEU P 47 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N VAL P 49 " --> pdb=" O SER P 64 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU P 66 " --> pdb=" O VAL P 49 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LYS P 79 " --> pdb=" O VAL P 65 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE P 67 " --> pdb=" O LYS P 79 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL P 81 " --> pdb=" O ILE P 67 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA P 96 " --> pdb=" O VAL P 80 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'P' and resid 54 through 56 removed outlier: 7.485A pdb=" N GLU P 70 " --> pdb=" O VAL P 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= BL Processing sheet with id= BM, first strand: chain 'Q' and resid 20 through 22 removed outlier: 6.853A pdb=" N LEU Q 36 " --> pdb=" O VAL Q 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= BM Processing sheet with id= BN, first strand: chain 'Q' and resid 26 through 28 removed outlier: 6.280A pdb=" N LEU Q 42 " --> pdb=" O ALA Q 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= BN Processing sheet with id= BO, first strand: chain 'Q' and resid 31 through 33 removed outlier: 6.076A pdb=" N SER Q 64 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL Q 49 " --> pdb=" O SER Q 64 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU Q 66 " --> pdb=" O VAL Q 49 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LYS Q 79 " --> pdb=" O VAL Q 65 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ILE Q 67 " --> pdb=" O LYS Q 79 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL Q 81 " --> pdb=" O ILE Q 67 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA Q 96 " --> pdb=" O VAL Q 80 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'Q' and resid 54 through 56 removed outlier: 7.485A pdb=" N GLU Q 70 " --> pdb=" O VAL Q 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= BP Processing sheet with id= BQ, first strand: chain 'R' and resid 20 through 22 removed outlier: 6.855A pdb=" N LEU R 36 " --> pdb=" O VAL R 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= BQ Processing sheet with id= BR, first strand: chain 'R' and resid 26 through 28 removed outlier: 6.280A pdb=" N LEU R 42 " --> pdb=" O ALA R 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= BR Processing sheet with id= BS, first strand: chain 'R' and resid 31 through 33 removed outlier: 6.076A pdb=" N SER R 64 " --> pdb=" O LEU R 47 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N VAL R 49 " --> pdb=" O SER R 64 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU R 66 " --> pdb=" O VAL R 49 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LYS R 79 " --> pdb=" O VAL R 65 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ILE R 67 " --> pdb=" O LYS R 79 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL R 81 " --> pdb=" O ILE R 67 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA R 96 " --> pdb=" O VAL R 80 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'R' and resid 54 through 56 removed outlier: 7.484A pdb=" N GLU R 70 " --> pdb=" O VAL R 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= BT Processing sheet with id= BU, first strand: chain 'S' and resid 20 through 22 removed outlier: 6.854A pdb=" N LEU S 36 " --> pdb=" O VAL S 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= BU Processing sheet with id= BV, first strand: chain 'S' and resid 26 through 28 removed outlier: 6.281A pdb=" N LEU S 42 " --> pdb=" O ALA S 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= BV Processing sheet with id= BW, first strand: chain 'S' and resid 31 through 33 removed outlier: 6.076A pdb=" N SER S 64 " --> pdb=" O LEU S 47 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL S 49 " --> pdb=" O SER S 64 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU S 66 " --> pdb=" O VAL S 49 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LYS S 79 " --> pdb=" O VAL S 65 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ILE S 67 " --> pdb=" O LYS S 79 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL S 81 " --> pdb=" O ILE S 67 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA S 96 " --> pdb=" O VAL S 80 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'S' and resid 54 through 56 removed outlier: 7.486A pdb=" N GLU S 70 " --> pdb=" O VAL S 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= BX Processing sheet with id= BY, first strand: chain 'T' and resid 20 through 22 removed outlier: 6.853A pdb=" N LEU T 36 " --> pdb=" O VAL T 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= BY Processing sheet with id= BZ, first strand: chain 'T' and resid 26 through 28 removed outlier: 6.279A pdb=" N LEU T 42 " --> pdb=" O ALA T 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= BZ Processing sheet with id= CA, first strand: chain 'T' and resid 31 through 33 removed outlier: 6.077A pdb=" N SER T 64 " --> pdb=" O LEU T 47 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N VAL T 49 " --> pdb=" O SER T 64 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU T 66 " --> pdb=" O VAL T 49 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LYS T 79 " --> pdb=" O VAL T 65 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE T 67 " --> pdb=" O LYS T 79 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL T 81 " --> pdb=" O ILE T 67 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA T 96 " --> pdb=" O VAL T 80 " (cutoff:3.500A) Processing sheet with id= CB, first strand: chain 'T' and resid 54 through 56 removed outlier: 7.484A pdb=" N GLU T 70 " --> pdb=" O VAL T 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= CB Processing sheet with id= CC, first strand: chain 'U' and resid 20 through 22 removed outlier: 6.853A pdb=" N LEU U 36 " --> pdb=" O VAL U 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= CC Processing sheet with id= CD, first strand: chain 'U' and resid 26 through 28 removed outlier: 6.280A pdb=" N LEU U 42 " --> pdb=" O ALA U 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= CD Processing sheet with id= CE, first strand: chain 'U' and resid 31 through 33 removed outlier: 6.076A pdb=" N SER U 64 " --> pdb=" O LEU U 47 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N VAL U 49 " --> pdb=" O SER U 64 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU U 66 " --> pdb=" O VAL U 49 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LYS U 79 " --> pdb=" O VAL U 65 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ILE U 67 " --> pdb=" O LYS U 79 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL U 81 " --> pdb=" O ILE U 67 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA U 96 " --> pdb=" O VAL U 80 " (cutoff:3.500A) Processing sheet with id= CF, first strand: chain 'U' and resid 54 through 56 removed outlier: 7.486A pdb=" N GLU U 70 " --> pdb=" O VAL U 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= CF Processing sheet with id= CG, first strand: chain 'V' and resid 20 through 22 removed outlier: 6.855A pdb=" N LEU V 36 " --> pdb=" O VAL V 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= CG Processing sheet with id= CH, first strand: chain 'V' and resid 26 through 28 removed outlier: 6.279A pdb=" N LEU V 42 " --> pdb=" O ALA V 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= CH Processing sheet with id= CI, first strand: chain 'V' and resid 31 through 33 removed outlier: 6.076A pdb=" N SER V 64 " --> pdb=" O LEU V 47 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL V 49 " --> pdb=" O SER V 64 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU V 66 " --> pdb=" O VAL V 49 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LYS V 79 " --> pdb=" O VAL V 65 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE V 67 " --> pdb=" O LYS V 79 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL V 81 " --> pdb=" O ILE V 67 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA V 96 " --> pdb=" O VAL V 80 " (cutoff:3.500A) Processing sheet with id= CJ, first strand: chain 'V' and resid 54 through 56 removed outlier: 7.485A pdb=" N GLU V 70 " --> pdb=" O VAL V 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= CJ 66 hydrogen bonds defined for protein. 132 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.61 Time building geometry restraints manager: 6.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5764 1.34 - 1.45: 1804 1.45 - 1.57: 8866 1.57 - 1.68: 0 1.68 - 1.80: 44 Bond restraints: 16478 Sorted by residual: bond pdb=" CA GLU S 74 " pdb=" CB GLU S 74 " ideal model delta sigma weight residual 1.524 1.499 0.024 1.33e-02 5.65e+03 3.35e+00 bond pdb=" CA GLU Q 74 " pdb=" CB GLU Q 74 " ideal model delta sigma weight residual 1.524 1.500 0.024 1.33e-02 5.65e+03 3.27e+00 bond pdb=" CA GLU C 74 " pdb=" CB GLU C 74 " ideal model delta sigma weight residual 1.524 1.500 0.024 1.33e-02 5.65e+03 3.26e+00 bond pdb=" CA GLU A 74 " pdb=" CB GLU A 74 " ideal model delta sigma weight residual 1.524 1.500 0.024 1.33e-02 5.65e+03 3.26e+00 bond pdb=" CA GLU K 74 " pdb=" CB GLU K 74 " ideal model delta sigma weight residual 1.524 1.500 0.024 1.33e-02 5.65e+03 3.25e+00 ... (remaining 16473 not shown) Histogram of bond angle deviations from ideal: 101.56 - 107.54: 760 107.54 - 113.51: 8899 113.51 - 119.49: 4197 119.49 - 125.47: 8276 125.47 - 131.44: 66 Bond angle restraints: 22198 Sorted by residual: angle pdb=" CA ARG I 59 " pdb=" CB ARG I 59 " pdb=" CG ARG I 59 " ideal model delta sigma weight residual 114.10 120.21 -6.11 2.00e+00 2.50e-01 9.32e+00 angle pdb=" CA ARG U 59 " pdb=" CB ARG U 59 " pdb=" CG ARG U 59 " ideal model delta sigma weight residual 114.10 120.15 -6.05 2.00e+00 2.50e-01 9.15e+00 angle pdb=" CA ARG E 59 " pdb=" CB ARG E 59 " pdb=" CG ARG E 59 " ideal model delta sigma weight residual 114.10 120.14 -6.04 2.00e+00 2.50e-01 9.13e+00 angle pdb=" CA ARG M 59 " pdb=" CB ARG M 59 " pdb=" CG ARG M 59 " ideal model delta sigma weight residual 114.10 120.13 -6.03 2.00e+00 2.50e-01 9.11e+00 angle pdb=" CA ARG Q 59 " pdb=" CB ARG Q 59 " pdb=" CG ARG Q 59 " ideal model delta sigma weight residual 114.10 120.12 -6.02 2.00e+00 2.50e-01 9.05e+00 ... (remaining 22193 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.17: 8680 17.17 - 34.33: 824 34.33 - 51.50: 242 51.50 - 68.66: 176 68.66 - 85.83: 44 Dihedral angle restraints: 9966 sinusoidal: 3916 harmonic: 6050 Sorted by residual: dihedral pdb=" CA ALA A 101 " pdb=" C ALA A 101 " pdb=" N GLY A 102 " pdb=" CA GLY A 102 " ideal model delta harmonic sigma weight residual -180.00 -158.76 -21.24 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA ALA H 101 " pdb=" C ALA H 101 " pdb=" N GLY H 102 " pdb=" CA GLY H 102 " ideal model delta harmonic sigma weight residual -180.00 -158.76 -21.24 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA ALA D 101 " pdb=" C ALA D 101 " pdb=" N GLY D 102 " pdb=" CA GLY D 102 " ideal model delta harmonic sigma weight residual -180.00 -158.76 -21.24 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 9963 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1368 0.032 - 0.065: 626 0.065 - 0.097: 367 0.097 - 0.130: 222 0.130 - 0.162: 101 Chirality restraints: 2684 Sorted by residual: chirality pdb=" CA VAL P 71 " pdb=" N VAL P 71 " pdb=" C VAL P 71 " pdb=" CB VAL P 71 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.58e-01 chirality pdb=" CA VAL T 71 " pdb=" N VAL T 71 " pdb=" C VAL T 71 " pdb=" CB VAL T 71 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.54e-01 chirality pdb=" CA VAL A 71 " pdb=" N VAL A 71 " pdb=" C VAL A 71 " pdb=" CB VAL A 71 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.54e-01 ... (remaining 2681 not shown) Planarity restraints: 2904 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 18 " 0.009 2.00e-02 2.50e+03 1.73e-02 3.00e+00 pdb=" C ASP B 18 " -0.030 2.00e-02 2.50e+03 pdb=" O ASP B 18 " 0.011 2.00e-02 2.50e+03 pdb=" N THR B 19 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP T 18 " -0.009 2.00e-02 2.50e+03 1.71e-02 2.93e+00 pdb=" C ASP T 18 " 0.030 2.00e-02 2.50e+03 pdb=" O ASP T 18 " -0.011 2.00e-02 2.50e+03 pdb=" N THR T 19 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP H 18 " -0.009 2.00e-02 2.50e+03 1.71e-02 2.93e+00 pdb=" C ASP H 18 " 0.030 2.00e-02 2.50e+03 pdb=" O ASP H 18 " -0.011 2.00e-02 2.50e+03 pdb=" N THR H 19 " -0.010 2.00e-02 2.50e+03 ... (remaining 2901 not shown) Histogram of nonbonded interaction distances: 0.56 - 1.43: 20 1.43 - 2.30: 40 2.30 - 3.17: 12178 3.17 - 4.03: 42757 4.03 - 4.90: 78621 Warning: very small nonbonded interaction distances. Nonbonded interactions: 133616 Sorted by model distance: nonbonded pdb=" OE1 GLU A 98 " pdb=" O GLU T 100 " model vdw 0.563 3.040 nonbonded pdb=" O GLU P 100 " pdb=" OE1 GLU S 98 " model vdw 0.563 3.040 nonbonded pdb=" O GLU L 100 " pdb=" OE1 GLU O 98 " model vdw 0.563 3.040 nonbonded pdb=" O GLU D 100 " pdb=" OE1 GLU G 98 " model vdw 0.563 3.040 nonbonded pdb=" O GLU H 100 " pdb=" OE1 GLU K 98 " model vdw 0.564 3.040 ... (remaining 133611 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 10208 2.51 5 N 2926 2.21 5 O 3212 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 7.380 Check model and map are aligned: 0.230 Process input model: 44.380 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Set scattering table: 0.150 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6562 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.039 16478 Z= 0.511 Angle : 1.117 6.531 22198 Z= 0.630 Chirality : 0.058 0.162 2684 Planarity : 0.004 0.017 2904 Dihedral : 18.477 85.829 6138 Min Nonbonded Distance : 0.563 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.15 % Favored : 89.85 % Rotamer Outliers : 9.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.68 (0.13), residues: 2178 helix: None (None), residues: 0 sheet: -3.45 (0.12), residues: 1122 loop : -4.09 (0.13), residues: 1056 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 532 time to evaluate : 1.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 154 outliers final: 20 residues processed: 608 average time/residue: 0.4745 time to fit residues: 370.5072 Evaluate side-chains 281 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 261 time to evaluate : 1.924 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.2956 time to fit residues: 11.0963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 7.9990 chunk 166 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 chunk 56 optimal weight: 7.9990 chunk 112 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 172 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 chunk 199 optimal weight: 0.8980 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 91 GLN K 95 GLN N 95 GLN ** T 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6712 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.040 16478 Z= 0.374 Angle : 0.761 7.354 22198 Z= 0.396 Chirality : 0.051 0.150 2684 Planarity : 0.005 0.043 2904 Dihedral : 6.229 20.472 2376 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 18.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.90 (0.15), residues: 2178 helix: None (None), residues: 0 sheet: -3.77 (0.10), residues: 1694 loop : -2.91 (0.23), residues: 484 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 329 time to evaluate : 2.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 329 average time/residue: 0.4805 time to fit residues: 202.8056 Evaluate side-chains 245 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 1.915 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 111 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 166 optimal weight: 6.9990 chunk 136 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 200 optimal weight: 10.0000 chunk 216 optimal weight: 0.6980 chunk 178 optimal weight: 9.9990 chunk 198 optimal weight: 9.9990 chunk 68 optimal weight: 7.9990 chunk 160 optimal weight: 10.0000 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 95 GLN F 68 HIS G 95 GLN H 68 HIS ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 68 HIS I 95 GLN J 68 HIS K 95 GLN N 95 GLN O 68 HIS ** P 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 68 HIS Q 68 HIS R 95 GLN S 68 HIS ** T 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 68 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.5627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.042 16478 Z= 0.437 Angle : 0.805 8.017 22198 Z= 0.425 Chirality : 0.053 0.179 2684 Planarity : 0.006 0.044 2904 Dihedral : 6.755 25.113 2376 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 22.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.09 % Favored : 86.91 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.85 (0.15), residues: 2178 helix: None (None), residues: 0 sheet: -3.72 (0.11), residues: 1452 loop : -3.59 (0.19), residues: 726 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 292 time to evaluate : 1.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 292 average time/residue: 0.4767 time to fit residues: 178.2377 Evaluate side-chains 216 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 1.995 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 197 optimal weight: 0.9980 chunk 150 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 95 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 chunk 200 optimal weight: 10.0000 chunk 212 optimal weight: 9.9990 chunk 104 optimal weight: 6.9990 chunk 190 optimal weight: 8.9990 chunk 57 optimal weight: 0.7980 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN B 95 GLN ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 95 GLN ** T 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6758 moved from start: 0.6084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.038 16478 Z= 0.342 Angle : 0.729 6.810 22198 Z= 0.380 Chirality : 0.051 0.152 2684 Planarity : 0.004 0.057 2904 Dihedral : 6.296 24.675 2376 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 21.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.20 % Favored : 88.80 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.60 (0.16), residues: 2178 helix: None (None), residues: 0 sheet: -3.68 (0.13), residues: 1232 loop : -3.52 (0.16), residues: 946 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 298 time to evaluate : 2.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 298 average time/residue: 0.5132 time to fit residues: 196.4262 Evaluate side-chains 228 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 228 time to evaluate : 1.932 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 177 optimal weight: 6.9990 chunk 120 optimal weight: 10.0000 chunk 3 optimal weight: 8.9990 chunk 158 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 181 optimal weight: 7.9990 chunk 146 optimal weight: 0.3980 chunk 0 optimal weight: 30.0000 chunk 108 optimal weight: 6.9990 chunk 190 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 overall best weight: 5.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 95 GLN ** P 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 moved from start: 0.6837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.051 16478 Z= 0.493 Angle : 0.851 7.847 22198 Z= 0.455 Chirality : 0.054 0.174 2684 Planarity : 0.006 0.049 2904 Dihedral : 7.093 24.460 2376 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 28.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.10 % Favored : 80.90 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.53 (0.16), residues: 2178 helix: None (None), residues: 0 sheet: -4.12 (0.13), residues: 1122 loop : -2.96 (0.16), residues: 1056 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 281 time to evaluate : 1.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 281 average time/residue: 0.5033 time to fit residues: 180.3338 Evaluate side-chains 226 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 1.889 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 71 optimal weight: 5.9990 chunk 191 optimal weight: 0.9980 chunk 42 optimal weight: 9.9990 chunk 124 optimal weight: 0.2980 chunk 52 optimal weight: 5.9990 chunk 212 optimal weight: 20.0000 chunk 176 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 70 optimal weight: 0.7980 chunk 111 optimal weight: 6.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN B 95 GLN E 68 HIS H 95 GLN ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6721 moved from start: 0.6788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 16478 Z= 0.206 Angle : 0.690 7.862 22198 Z= 0.344 Chirality : 0.051 0.165 2684 Planarity : 0.003 0.038 2904 Dihedral : 5.577 24.188 2376 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 19.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.56 (0.15), residues: 2178 helix: None (None), residues: 0 sheet: -3.61 (0.13), residues: 1298 loop : -3.47 (0.17), residues: 880 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 303 time to evaluate : 2.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 303 average time/residue: 0.4764 time to fit residues: 184.7742 Evaluate side-chains 224 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 2.005 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 205 optimal weight: 10.0000 chunk 23 optimal weight: 40.0000 chunk 121 optimal weight: 0.7980 chunk 155 optimal weight: 9.9990 chunk 120 optimal weight: 4.9990 chunk 179 optimal weight: 9.9990 chunk 118 optimal weight: 8.9990 chunk 212 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 129 optimal weight: 8.9990 chunk 97 optimal weight: 5.9990 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 95 GLN ** N 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.7429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.057 16478 Z= 0.515 Angle : 0.889 8.730 22198 Z= 0.473 Chirality : 0.055 0.164 2684 Planarity : 0.006 0.055 2904 Dihedral : 7.090 25.129 2376 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 30.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.22 % Favored : 77.78 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.64 (0.15), residues: 2178 helix: None (None), residues: 0 sheet: -3.92 (0.13), residues: 1100 loop : -3.43 (0.15), residues: 1078 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 282 time to evaluate : 2.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 0.4979 time to fit residues: 179.4464 Evaluate side-chains 227 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 227 time to evaluate : 1.916 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.5844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 131 optimal weight: 2.9990 chunk 84 optimal weight: 0.3980 chunk 126 optimal weight: 0.4980 chunk 63 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 134 optimal weight: 1.9990 chunk 144 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 166 optimal weight: 4.9990 chunk 192 optimal weight: 8.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN B 95 GLN E 91 GLN ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6700 moved from start: 0.7260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 16478 Z= 0.191 Angle : 0.725 7.637 22198 Z= 0.356 Chirality : 0.052 0.166 2684 Planarity : 0.003 0.037 2904 Dihedral : 5.444 23.732 2376 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 18.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.65 (0.16), residues: 2178 helix: None (None), residues: 0 sheet: -3.68 (0.12), residues: 1408 loop : -3.33 (0.18), residues: 770 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 288 time to evaluate : 1.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 288 average time/residue: 0.5144 time to fit residues: 188.8951 Evaluate side-chains 220 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 2.059 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 203 optimal weight: 5.9990 chunk 185 optimal weight: 9.9990 chunk 197 optimal weight: 9.9990 chunk 118 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 chunk 155 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 chunk 178 optimal weight: 5.9990 chunk 186 optimal weight: 2.9990 chunk 196 optimal weight: 10.0000 chunk 129 optimal weight: 5.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 95 GLN ** P 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6797 moved from start: 0.7620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.052 16478 Z= 0.417 Angle : 0.841 8.665 22198 Z= 0.439 Chirality : 0.054 0.228 2684 Planarity : 0.005 0.054 2904 Dihedral : 6.574 29.092 2376 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 26.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.66 % Favored : 79.34 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.69 (0.16), residues: 2178 helix: None (None), residues: 0 sheet: -3.82 (0.12), residues: 1298 loop : -3.33 (0.17), residues: 880 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 2.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.5139 time to fit residues: 178.2668 Evaluate side-chains 231 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 2.126 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 208 optimal weight: 7.9990 chunk 127 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 chunk 145 optimal weight: 0.0270 chunk 219 optimal weight: 30.0000 chunk 201 optimal weight: 9.9990 chunk 174 optimal weight: 0.9990 chunk 18 optimal weight: 10.0000 chunk 134 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 138 optimal weight: 0.9980 overall best weight: 0.7642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN G 95 GLN ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6678 moved from start: 0.7491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 16478 Z= 0.182 Angle : 0.748 10.157 22198 Z= 0.364 Chirality : 0.052 0.212 2684 Planarity : 0.003 0.065 2904 Dihedral : 5.177 22.764 2376 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.23 (0.16), residues: 2178 helix: None (None), residues: 0 sheet: -3.44 (0.13), residues: 1298 loop : -3.17 (0.17), residues: 880 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 272 time to evaluate : 2.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 272 average time/residue: 0.4982 time to fit residues: 173.6554 Evaluate side-chains 212 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 2.015 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.7225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 9.9990 chunk 53 optimal weight: 8.9990 chunk 160 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 48 optimal weight: 0.6980 chunk 174 optimal weight: 9.9990 chunk 73 optimal weight: 8.9990 chunk 179 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 153 optimal weight: 6.9990 overall best weight: 7.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4794 r_free = 0.4794 target = 0.105067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.078823 restraints weight = 35592.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.080093 restraints weight = 25781.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.081083 restraints weight = 20040.389| |-----------------------------------------------------------------------------| r_work (final): 0.4271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.8165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.072 16478 Z= 0.665 Angle : 1.052 10.017 22198 Z= 0.564 Chirality : 0.060 0.219 2684 Planarity : 0.007 0.084 2904 Dihedral : 7.801 31.931 2376 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 35.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 25.62 % Favored : 74.38 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.41 (0.15), residues: 2178 helix: None (None), residues: 0 sheet: -4.00 (0.15), residues: 946 loop : -3.26 (0.14), residues: 1232 =============================================================================== Job complete usr+sys time: 3901.57 seconds wall clock time: 71 minutes 7.51 seconds (4267.51 seconds total)